Ligand discovery and gene delivery via retroviral surface display

Abstract

Disclosed herein are compositions of retroviruses and methods of using the same for gene delivery, wherein the retroviruses comprise a viral envelope protein comprising at least one mutation that diminishes its native function, a non-viral membrane-bound protein comprising a membrane-bound domain and an extracellular targeting domain.

1 .- 15 . (canceled) 
     
     
         16 . A composition comprising a lentivirus, the lentivirus comprising:
 (a) a nucleic acid;   (b) a viral envelope comprising   
       (i) a vesicular stomatitis virus (VSV)-G envelope protein comprising an amino acid sequence at least 95% identical to SEQ ID NO: 13, wherein the VSV-G envelope protein comprises one or more amino acid mutations at position 47 (lysine, K) and/or position 354 (arginine, R), wherein the amino acid mutation(s) diminish the native viral tropism of the VSV-G envelope protein compared to the non-mutated VSV-G envelope protein; and 
       (ii) a non-viral membrane-bound protein comprising a transmembrane-domain and an extracellular targeting domain that binds to a ligand expressed on the surface of a T cell or a B cell. 
     
     
         17 . The composition of  claim 16 , wherein the nucleic acid encodes an mRNA, a double-stranded DNA, an antisense RNA, a microRNA, a gene of interest, or a protein. 
     
     
         18 . The composition of  claim 16 , wherein the one or more amino acid mutations comprise an amino acid mutation at position K47 or position R354. 
     
     
         19 . The composition of  claim 16 , wherein the one or more amino acid mutations comprise an amino acid mutation at position K47 and position R354. 
     
     
         20 . The composition of  claim 16 , wherein the one or more amino acid mutations comprise a K47A or K47Q amino acid substitution and/or an R354A or R354Q amino acid substitution. 
     
     
         21 . The composition of  claim 16 , wherein the extracellular targeting domain comprises a protein, a peptide, or an antibody. 
     
     
         22 . The composition of  claim 21 , wherein the extracellular targeting domain comprises an interleukin-13 protein domain, a CD80 protein domain, a full-length antibody, an antibody fragment, a nanobody, a single chain antibody (scFv), an anti-CD19 antibody, an anti-TCR antibody, or an anti-CD3 antibody. 
     
     
         23 . The lentivirus of  claim 16 , wherein the ligand comprises a T cell receptor (TCR), a cytokine receptor, a cytokine, a T cell surface marker, CD3, CD19, or CD20. 
     
     
         24 . A method of delivering a nucleic acid to a T cell or B cell, the method comprising:
 (a) providing a composition comprising a lentivirus, the lentivirus comprising: a nucleic acid and a viral envelope comprising (i) a VSV-G envelope protein comprising an amino acid sequence at least 95% identical to SEQ ID NO: 13, wherein the VSV-G envelope protein comprises one or more amino acid mutations at position 47 (lysine, K) and/or position 354 (arginine, R), wherein the amino acid mutation(s) diminish the native viral tropism of the VSV-G envelope protein compared to the non-mutated VSV-G envelope protein; and (ii) a non-viral membrane-bound protein comprising a transmembrane-domain and an extracellular targeting domain that binds to a ligand expressed on the surface of a T cell or a B cell;   (b) contacting the composition with the T cell or B cell,   thereby delivering the nucleic acid to the T cell or B cell.   
     
     
         25 . The method of  claim 24 , wherein the nucleic acid encodes an mRNA, a double-stranded DNA, an antisense RNA, a microRNA, a gene of interest, or a protein. 
     
     
         26 . The method of  claim 24 , wherein the one or more amino acid mutations comprise an amino acid mutation at position K47 or position R354. 
     
     
         27 . The method of  claim 24 , wherein the one or more amino acid mutations comprise an amino acid mutation at position K47 and position R354. 
     
     
         28 . The method of  claim 24 , wherein the one or more amino acid mutations comprise a K47A or K47Q amino acid substitution and/or an R354A or R354Q amino acid substitution. 
     
     
         29 . The method of  claim 24 , wherein the extracellular targeting domain comprises a protein, a peptide, or an antibody. 
     
     
         30 . The method of  claim 29 , wherein the extracellular targeting domain comprises an interleukin-13 protein domain, a CD80 protein domain, a full-length antibody, an antibody fragment, a nanobody, an scFv, an anti-CD19 antibody, an anti-TCR antibody, or an anti-CD3 antibody. 
     
     
         31 . The method of  claim 24 , wherein the ligand comprises a T cell receptor (TCR), a cytokine receptor, a cytokine, a T cell surface marker, CD3, CD19, or CD20. 
     
     
         32 . A composition comprising a lentivirus, the lentivirus comprising
 (a) a nucleic acid;   (b) a viral envelope comprising:   (i) a VSV-G envelope protein comprising an amino acid sequence at least 95% identical to SEQ ID NO: 13, wherein the VSV-G envelope protein comprises one or more amino acid mutations at position 47 (lysine, K) and/or position 354 (arginine, R), wherein the amino acid mutation(s) diminish the native viral tropism of the VSV-G envelope protein compared to the non-mutated VSV-G envelope protein; and   (ii) a non-viral membrane-bound protein comprising a transmembrane domain and an extracellular targeting domain that comprises an anti-CD3 antibody.   
     
     
         33 . The composition of  claim 32 , wherein the nucleic acid encodes an mRNA, a double-stranded DNA, an antisense RNA, a microRNA, a gene of interest, or a protein. 
     
     
         34 . The composition of  claim 32 , wherein the one or more amino acid mutations comprise an amino acid mutation at position K47 or position R354. 
     
     
         35 . The composition of  claim 32 , wherein the one or more amino acid mutations comprise an amino acid mutation at position K47 and position R354. 
     
     
         36 . The composition of  claim 32 , wherein the one or more amino acid mutations comprise a K47A or K47Q amino acid substitution and/or an R354A or R354Q amino acid substitution. 
     
     
         37 . The composition of  claim 32 , wherein the viral envelope further comprises a non-viral membrane-bound protein comprising a transmembrane domain and an extracellular targeting domain that comprises a full-length antibody, an antibody fragment, a nanobody, an scFv, or an anti-TCR antibody. 
     
     
         38 . The composition of  claim 32 , wherein the viral envelope further comprises a non-viral membrane-bound protein that comprises a CD80 protein comprising a CD80 extracellular domain and a transmembrane domain. 
     
     
         39 . A method of delivering a nucleic acid to a T cell, the method comprising:
 (a) providing a composition comprising a lentivirus, the lentivirus comprising: a nucleic acid and a viral envelope comprising (i) a VSV-G envelope protein comprising an amino acid sequence at least 95% identical to SEQ ID NO: 13, wherein the VSV-G envelope protein comprises one or more amino acid mutations at position 47 (lysine, K) and/or position 354 (arginine, R), wherein the amino acid mutation(s) diminish the native viral tropism of the VSV-G envelope protein compared to the non-mutated VSV-G envelope protein; and (ii) a non-viral membrane-bound protein comprising a transmembrane domain and an extracellular targeting domain that comprises an anti-CD3 antibody;   (b) contacting the lentivirus with the T cell,   thereby delivering the nucleic acid to the T cell.   
     
     
         40 . The method of  claim 39 , wherein the nucleic acid encodes an mRNA, a double-stranded DNA, an antisense RNA, a microRNA, a gene of interest, or a protein. 
     
     
         41 . The method of  claim 39 , wherein the one or more amino acid mutations comprise an amino acid mutation at position K47 or position R354. 
     
     
         42 . The method of  claim 39 , wherein the one or more amino acid mutations comprise an amino acid mutation at position K47 and position R354. 
     
     
         43 . The method of  claim 39 , wherein the one or more amino acid mutations comprise a K47A or K47Q amino acid substitution and/or an R354A or R354Q amino acid substitution. 
     
     
         44 . The method of  claim 39 , wherein the viral envelope further comprises a non-viral membrane-bound protein comprising a transmembrane domain and an extracellular targeting domain that comprises a full-length antibody, an antibody fragment, a nanobody, an scFv, or an anti-TCR antibody. 
     
     
         45 . The method of  claim 39 , wherein the viral envelope further comprises a non-viral membrane-bound protein that comprises a CD80 protein comprising a CD80 extracellular domain and a transmembrane domain.